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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ), 'gf_id' => 'HOM05D001148', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001148' ), 'data_identifier' => 'HOM05D001148', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001148', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '541', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p27230' => 'bna', 'A02p37680' => 'bna', 'A05p28450' => 'bna', 'A06p38990' => 'bna', 'A09p64270' => 'bna', 'Aa31LG1G2820' => 'aar', 'Aa31LG7G3550' => 'aar', 'Aa31LG8G7260' => 'aar', 'Aa31sc661G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3335' => 'aag', 'Actinidia05080' => 'ach', 'Actinidia09722' => 'ach', 'Actinidia11863' => 'ach', 'Actinidia30060' => 'ach', 'Actinidia31463' => 'ach', 'Ah.01g014640' => 'amhyb', 'Ah.06g182630' => 'amhyb', 'Ah.06g190420' => 'amhyb', 'Ah.08g214550' => 'amhyb', 'Ah.09g234670' => 'amhyb', 'Ah.15g093950' => 'amhyb', 'AL1G23080' => 'aly', 'AL219U10020' => 'aly', 'AL3G18450' => 'aly', 'AL3G34170' => 'aly', 'AL8G18690' => 'aly', 'AL8G21720' => 'aly', 'Aqoxy1G03109' => 'aox', 'Aqoxy1G03338' => 'aox', 'Aqoxy2G03903' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4BNM0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6MJ9X7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8KT0CJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AQ7EBY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD7RPV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2G4TQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HB650C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IAB8I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L8E2ZZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LUS7PI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M2LW4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S3VQUL' => 'arhy', 'AT1G11905' => 'ath', 'AT3G07190' => 'ath', 'AT3G20450' => 'ath', 'AT5G42570' => 'ath', 'AT5G48660' => 'ath', 'ATR0069G015' => 'atr', 'ATR0589G123' => 'atr', 'Atru.chr10.2258' => 'acertr', 'Atru.chr2.3485' => 'acertr', 'Atru.chr6.1418' => 'acertr', 'Atru.chr6.3211' => 'acertr', 'AUR62001120' => 'cqu', 'AUR62012734' => 'cqu', 'AUR62015814' => 'cqu', 'AUR62016556' => 'cqu', 'AUR62020402' => 'cqu', 'AUR62021920' => 'cqu', 'AUR62025072' => 'cqu', 'AUR62037147' => 'cqu', 'BcaB06g26112' => 'bca', 'BcaB07g30040' => 'bca', 'BcaB07g30612' => 'bca', 'BcaB08g37423' => 'bca', 'BcaC03g16531' => 'bca', 'BcaC03g17670' => 'bca', 'BcaC05g28332' => 'bca', 'BcaC06g30769' => 'bca', 'BcaC06g30770' => 'bca', 'BolC2t10402H' => 'bol', 'BolC2t11745H' => 'bol', 'BolC4t24033H' => 'bol', 'BolC5t33105H' => 'bol', 'BolC7t44454H' => 'bol', 'BolC8t52325H' => 'bol', 'BraA02t07739Z' => 'bra', 'BraA02t08750Z' => 'bra', 'BraA05t21724Z' => 'bra', 'BraA06t26813Z' => 'bra', 'C02p43450' => 'bna', 'C02p56770' => 'bna', 'C04p25270' => 'bna', 'C05p43890' => 'bna', 'C07p39340' => 'bna', 'C08p47880' => 'bna', 'CAN.G1003.10' => 'can', 'CAN.G1014.19' => 'can', 'CAN.G123.9' => 'can', 'CAN.G260.6' => 'can', 'CAN.G283.2' => 'can', 'CAN.G332.8' => 'can', 'CANSAT01G1967' => 'cansat', 'CANSAT11G0558' => 'cansat', 'CANSAT56G2857' => 'cansat', 'CANSAT64G1181' => 'cansat', 'CARHR012230' => 'chi', 'CARHR081830' => 'chi', 'CARHR096190' => 'chi', 'CARHR181800' => 'chi', 'CARHR183250' => 'chi', 'Carub.0001s1157' => 'cru', 'Carub.0003s2039' => 'cru', 'Carub.0008s0645' => 'cru', 'Carub.0008s0838' => 'cru', 'Ca_00677_v3' => 'car', 'Ca_01609_v3' => 'car', 'Ca_19507_v3' => 'car', 'Ca_19511_v3' => 'car', 'Ca_24092_v3' => 'car', 'Ca_24093_v3' => 'car', 'Cc01_g16800' => 'ccan', 'Cc05_g04290' => 'ccan', 'Cc06_g20860' => 'ccan', 'Cc09_g01450' => 'ccan', 'CDE02G4758' => 'cde', 'CDE05G1151' => 'cde', 'Cfa000189' => 'cfa', 'Cfa004374' => 'cfa', 'Cfa014378' => 'cfa', 'Ciclev10009874m.g' => 'ccl', 'Ciclev10016599m.g' => 'ccl', 'Ciclev10016648m.g' => 'ccl', 'Ciclev10022165m.g' => 'ccl', 'CiPaw.01G049300' => 'cil', 'CiPaw.02G022700' => 'cil', 'CiPaw.04G114600' => 'cil', 'CiPaw.09G095100' => 'cil', 'CiPaw.11G192000' => 'cil', 'ClCG01G021810' => 'cla', 'ClCG02G008900' => 'cla', 'ClCG07G002030' => 'cla', 'ClCG09G019890' => 'cla', 'COL.COLO4_11254' => 'col', 'COL.COLO4_15640' => 'col', 'COL.COLO4_31803' => 'col', 'Cpa.g.sc152.33' => 'cpa', 'Cpa.g.sc8.128' => 'cpa', 'Cpa.g.sc87.95' => 'cpa', 'CsaV3_2G034830' => 'csa', 'CsaV3_3G029990' => 'csa', 'CsaV3_6G048860' => 'csa', 'CSS0006751' => 'camsi', 'CSS0010760' => 'camsi', 'CSS0032706' => 'camsi', 'CSS0035765' => 'camsi', 'DCAR_004228' => 'dca', 'DCAR_008165' => 'dca', 'DCAR_012661' => 'dca', 'DCAR_019760' => 'dca', 'DCAR_021166' => 'dca', 'DCAR_021167' => 'dca', 'Dinv05414' => 'din', 'Dinv12659' => 'din', 'Dinv13922' => 'din', 'Dinv19182' => 'din', 'Dinv20070' => 'din', 'Dinv39723' => 'din', 'Dinv40777' => 'din', 'Duzib133G1429' => 'dzi', 'Duzib138G1850' => 'dzi', 'Duzib160G0340' => 'dzi', 'Duzib211G0673' => 'dzi', 'Duzib213G1054' => 'dzi', 'Duzib235G1022' => 'dzi', 'Duzib268G0025' => 'dzi', 'Duzib268G1805' => 'dzi', 'Duzib268G1880' => 'dzi', 'ECA234G1371' => 'eca', 'ECA236G2164' => 'eca', 'ECA236G2251' => 'eca', 'ECA236G3255' => 'eca', 'ECA240G4458' => 'eca', 'EL10Ac4g07768' => 'bvu', 'EL10Ac4g07770' => 'bvu', 'EL10Ac7g17879' => 'bvu', 'EL10Ac8g20089' => 'bvu', 'EL10Ac9g22344' => 'bvu', 'Eucgr.A01117' => 'egr', 'Eucgr.E04024' => 'egr', 'Eucgr.F03480' => 'egr', 'Eucgr.H00780' => 'egr', 'FAN02G1807' => 'fan', 'FAN05G4903' => 'fan', 'FAN09G3943' => 'fan', 'FAN11G3210' => 'fan', 'FAN14G2143' => 'fan', 'FAN15G0721' => 'fan', 'FAN16G2362' => 'fan', 'FAN21G1972' => 'fan', 'FAN21G3955' => 'fan', 'FAN24G2152' => 'fan', 'FAN25G1474' => 'fan', 'FAN25G1513' => 'fan', 'FAN25G2416' => 'fan', 'FAN27G0607' => 'fan', 'FvH4_2g18660' => 'fve', 'FvH4_3g01741' => 'fve', 'FvH4_3g01750' => 'fve', 'FvH4_3g23110' => 'fve', 'FvH4_6g42950' => 'fve', 'Glyma.02G292600' => 'gma', 'Glyma.06G307200' => 'gma', 'Glyma.08G349600' => 'gma', 'Glyma.09G005400' => 'gma', 'Glyma.12G097500' => 'gma', 'Glyma.12G192600' => 'gma', 'Glyma.13G309800' => 'gma', 'Glyma.14G022000' => 'gma', 'Glyma.15G110000' => 'gma', 'Glyma.18G166700' => 'gma', 'Gohir.A01G081500' => 'ghi', 'Gohir.A01G081700' => 'ghi', 'Gohir.A01G081800' => 'ghi', 'Gohir.A01G081900' => 'ghi', 'Gohir.A01G082100' => 'ghi', 'Gohir.A06G149600' => 'ghi', 'Gohir.A06G206500' => 'ghi', 'Gohir.A07G199800' => 'ghi', 'Gohir.A08G195200' => 'ghi', 'Gohir.A10G012300' => 'ghi', 'Gohir.D01G068600' => 'ghi', 'Gohir.D01G068700' => 'ghi', 'Gohir.D06G155700' => 'ghi', 'Gohir.D06G215100' => 'ghi', 'Gohir.D07G206200' => 'ghi', 'Gohir.D08G212656' => 'ghi', 'Gohir.D10G011700' => 'ghi', 'Gorai.001G232500' => 'gra', 'Gorai.002G090600' => 'gra', 'Gorai.002G090900' => 'gra', 'Gorai.004G226500' => 'gra', 'Gorai.010G182000' => 'gra', 'Gorai.010G251300' => 'gra', 'Gorai.011G013000' => 'gra', 'GSVIVG01003255001' => 'vvi', 'GSVIVG01012687001' => 'vvi', 'GSVIVG01012689001' => 'vvi', 'GSVIVG01030445001' => 'vvi', 'GSVIVG01037893001' => 'vvi', 'HanXRQChr03g0076731' => 'han', 'HanXRQChr04g0108261' => 'han', 'HanXRQChr05g0129361' => 'han', 'HanXRQChr07g0189541' => 'han', 'HanXRQChr10g0307491' => 'han', 'HanXRQChr13g0408691' => 'han', 'HanXRQChr16g0506811' => 'han', 'Haze_06825' => 'cav', 'Haze_12838' => 'cav', 'Haze_12842' => 'cav', 'Haze_15038' => 'cav', 'Hma1.2p1_0039F.1_g024500' => 'hma', 'Hma1.2p1_0149F.1_g066340' => 'hma', 'Hma1.2p1_0226F.1_g095460' => 'hma', 'Hma1.2p1_0249F.1_g102240' => 'hma', 'Hma1.2p1_0298F.1_g117680' => 'hma', 'Hma1.2p1_2419F.1_g321810' => 'hma', 'HPP92_008834' => 'vpl', 'HPP92_013553' => 'vpl', 'Hund05571' => 'sun', 'Hund18424' => 'sun', 'Hund23449' => 'sun', 'Lalb_Chr01g0005731' => 'lal', 'Lalb_Chr01g0005741' => 'lal', 'Lalb_Chr01g0022241' => 'lal', 'Lalb_Chr01g0022251' => 'lal', 'Lalb_Chr03g0028641' => 'lal', 'Lalb_Chr03g0041551' => 'lal', 'Lalb_Chr04g0248301' => 'lal', 'Lalb_Chr18g0056531' => 'lal', 'Lalb_Chr19g0125781' => 'lal', 'Lalb_Chr19g0125791' => 'lal', 'Lalb_Chr19g0135991' => 'lal', 'Lalb_Chr20g0118791' => 'lal', 'Lalb_Chr24g0393251' => 'lal', 'Lj1A1233G61' => 'lonja', 'Lj1A768G23' => 'lonja', 'Lj1A88T39' => 'lonja', 'Lj1C768T1' => 'lonja', 'Lj1C768T2' => 'lonja', 'Lj1g0009415' => 'lja', 'Lj2A1127T49' => 'lonja', 'Lj2A266T58' => 'lonja', 'Lj3g0004433' => 'lja', 'Lj3g0017058' => 'lja', 'Lj3P122T14' => 'lonja', 'Lj6g0023794' => 'lja', 'Lj8A170T77' => 'lonja', 'LjContig00272g0010581' => 'lja', 'Lsat_1_v5_gn_5_124281' => 'lsa', 'Lsat_1_v5_gn_7_16580' => 'lsa', 'Lsat_1_v5_gn_7_98541' => 'lsa', 'Lsat_1_v5_gn_8_89541' => 'lsa', 'Lsat_1_v5_gn_9_107201' => 'lsa', 'Lsat_1_v5_gn_9_92380' => 'lsa', 'Manes.12G046700' => 'mes', 'Manes.12G073500' => 'mes', 'Manes.13G048200' => 'mes', 'Manes.13G068088' => 'mes', 'Manes.15G069100' => 'mes', 'Manes.16G004400' => 'mes', 'Manes.17G029048' => 'mes', 'Mapoly0006s0178' => 'mpo', 'MBI07_g25505_MAGBIO' => 'mbi', 'MBI07_g25512_MAGBIO' => 'mbi', 'MBI07_g28660_MAGBIO' => 'mbi', 'MBI07_g43171_MAGBIO' => 'mbi', 'MBI08_g05571_MAGBIO' => 'mbi', 'MBI10_g35590_MAGBIO' => 'mbi', 'MBI10_g40666_MAGBIO' => 'mbi', 'MBI11_g07439_MAGBIO' => 'mbi', 'MD00G1159100' => 'mdo', 'MD03G1197900' => 'mdo', 'MD05G1172500' => 'mdo', 'MD05G1349500' => 'mdo', 'MD09G1110800' => 'mdo', 'MD10G1160700' => 'mdo', 'MD10G1324100' => 'mdo', 'MD11G1213800' => 'mdo', 'MD17G1098700' => 'mdo', 'Medtr2g023880' => 'mtr', 'Medtr2g088060' => 'mtr', 'Medtr4g049540' => 'mtr', 'Medtr5g093360' => 'mtr', 'Medtr7g056133' => 'mtr', 'MELO3C000061.2' => 'cme', 'MELO3C001501.2' => 'cme', 'MELO3C001612.2' => 'cme', 'MELO3C007406.2' => 'cme', 'MELO3C019287.2' => 'cme', 'MELO3C021642.2' => 'cme', 'MELO3C022712.2' => 'cme', 'MELO3C028141.2' => 'cme', 'MELO3C035342.2' => 'cme', 'Migut.D02498' => 'egut', 'Migut.H01183' => 'egut', 'Migut.M01339' => 'egut', 'Migut.M01739' => 'egut', 'Migut.N00627' => 'egut', 'MSTRG.17998' => 'ama', 'MSTRG.18840' => 'ama', 'MSTRG.20965' => 'ama', 'MSTRG.6937' => 'ama', 'MSTRG.7195' => 'ama', 'Nitab4.5_0000005g0230' => 'nta', 'Nitab4.5_0000045g0410' => 'nta', 'Nitab4.5_0000168g0200' => 'nta', 'Nitab4.5_0000345g0020' => 'nta', 'Nitab4.5_0000575g0100' => 'nta', 'Nitab4.5_0000622g0230' => 'nta', 'Nitab4.5_0001409g0010' => 'nta', 'Nitab4.5_0003450g0020' => 'nta', 'Nitab4.5_0004712g0030' => 'nta', 'Nitab4.5_0006031g0050' => 'nta', 'Nitab4.5_0007644g0010' => 'nta', 'Nn1g03465' => 'nnu', 'Nn1g07207' => 'nnu', 'Nn1g07937' => 'nnu', 'Nn3g20040' => 'nnu', 'Oeu002745.1' => 'oeu', 'Oeu013834.1' => 'oeu', 'Oeu024918.1' => 'oeu', 'Oeu031827.1' => 'oeu', 'Oeu041834.1' => 'oeu', 'Oeu051203.1' => 'oeu', 'Oeu051888.1' => 'oeu', 'Os02g0321800' => 'osa', 'Os03g0848400' => 'osa', 'Os05g0272900' => 'osa', 'Os06g0367500' => 'osa', 'Os07g0291200' => 'osa', 'Peaxi162Scf00047g01924' => 'pax', 'Peaxi162Scf00178g01618' => 'pax', 'Peaxi162Scf00238g00026' => 'pax', 'Peaxi162Scf00307g01423' => 'pax', 'Peaxi162Scf00394g00021' => 'pax', 'Peaxi162Scf00660g00116' => 'pax', 'PGR031G0480' => 'pgr', 'PGR042G0008' => 'pgr', 'PGR042G1857' => 'pgr', 'PGR083G0562' => 'pgr', 'PGSC0003DMG400013903' => 'stu', 'PGSC0003DMG400016468' => 'stu', 'PGSC0003DMG400016907' => 'stu', 'PGSC0003DMG400017494' => 'stu', 'PGSC0003DMG400022061' => 'stu', 'Phvul.005G115800' => 'pvu', 'Phvul.006G148100' => 'pvu', 'Phvul.008G130500' => 'pvu', 'Phvul.008G269400' => 'pvu', 'Phvul.010G021100' => 'pvu', 'Phvul.011G102200' => 'pvu', 'Potri.002G245300' => 'ptr', 'Potri.004G007900' => 'ptr', 'Potri.011G007200' => 'ptr', 'Potri.011G089100' => 'ptr', 'Potri.014G154800' => 'ptr', 'Potri.014G191500' => 'ptr', 'Pp3c1_12950' => 'ppa', 'Prupe.3G215300' => 'ppe', 'Prupe.3G215400' => 'ppe', 'Prupe.3G215700' => 'ppe', 'Prupe.4G018100' => 'ppe', 'Prupe.4G217500' => 'ppe', 'Prupe.8G199900' => 'ppe', 'Psat0s1523g0120' => 'psa', 'Psat1g179160' => 'psa', 'Psat5g261720' => 'psa', 'Psat7g203000' => 'psa', 'PSO017G6073' => 'pso', 'PSO063G6769' => 'pso', 'PSO541G6235' => 'pso', 'PSO675G0868' => 'pso', 'QL03p040340' => 'qlo', 'QL04p004216' => 'qlo', 'QL05p000374' => 'qlo', 'QL05p072545' => 'qlo', 'QL08p009289' => 'qlo', 'QL08p032616' => 'qlo', 'QL09p051822' => 'qlo', 'QL09p051828' => 'qlo', 'QL09p052518' => 'qlo', 'QL09p052606' => 'qlo', 'QL09p052719' => 'qlo', 'RcHm_v2.0_Chr2g0158931' => 'rch', 'RcHm_v2.0_Chr5g0002591' => 'rch', 'RcHm_v2.0_Chr5g0040711' => 'rch', 'RcHm_v2.0_Chr5g0040761' => 'rch', 'RcHm_v2.0_Chr6g0284221' => 'rch', 'Rhsim04G0052600' => 'rsi', 'Rhsim06G0163700' => 'rsi', 'Rhsim06G0163800' => 'rsi', 'Rhsim06G0163900' => 'rsi', 'Rhsim06G0219800' => 'rsi', 'Rhsim13G0047100' => 'rsi', 'Rhsim13G0152200' => 'rsi', 'RhsimUnG0178200' => 'rsi', 'Sabra04G0004700' => 'sbr', 'Sabra11G0006300' => 'sbr', 'Sabra11G0009700' => 'sbr', 'Sabra11G0113900' => 'sbr', 'SalBow3G2166' => 'sbo', 'SalBow4G1782' => 'sbo', 'SalBow6G1794' => 'sbo', 'SalBow6G4344' => 'sbo', 'SalBow8G0928' => 'sbo', 'SalBow8G0947' => 'sbo', 'Sc05g0001990' => 'sci', 'Sc05g0009330' => 'sci', 'Sc12g0002260' => 'sci', 'Sc16g0005870' => 'sci', 'Sed0004848' => 'sed', 'Sed0004976' => 'sed', 'Sed0007150' => 'sed', 'Sed0022136' => 'sed', 'Sed0026031' => 'sed', 'Sed0027807' => 'sed', 'SEGI_04072' => 'sgi', 'SEGI_08663' => 'sgi', 'SEGI_09429' => 'sgi', 'SEGI_22010' => 'sgi', 'SEGI_27990' => 'sgi', 'SGA_v2.0_scaffold172G39009' => 'sas', 'SGA_v2.0_scaffold18G08330' => 'sas', 'SGA_v2.0_scaffold4G01904' => 'sas', 'SGA_v2.0_scaffold6G03496' => 'sas', 'SGA_v2.0_scaffold7G03808' => 'sas', 'SHI14560' => 'shi', 'SMO143G0031' => 'smo', 'Solyc01g060430.1' => 'sly', 'Solyc02g032930.3' => 'sly', 'Solyc02g080870.3' => 'sly', 'Solyc09g059570.3' => 'sly', 'Solyc10g053910.3' => 'sly', 'Solyc12g005910.2' => 'sly', 'Sopen02g011300' => 'spe', 'Sopen02g025560' => 'spe', 'Sopen09g022750' => 'spe', 'Sopen10g023750' => 'spe', 'Sopen12g001860' => 'spe', 'Sp1g10530' => 'spa', 'Sp2g06960' => 'spa', 'Sp2g19080' => 'spa', 'Sp3g06130' => 'spa', 'Sp3g18460' => 'spa', 'SpUn0014_0110' => 'spa', 'TAR362G1309' => 'tar', 'TAR365G1065' => 'tar', 'TAR624G0132' => 'tar', 'TAR629G0998' => 'tar', 'TAR636G0873' => 'tar', 'THA.LOC104809492' => 'tha', 'THA.LOC104817861' => 'tha', 'THA.LOC104818690' => 'tha', 'THA.LOC104820464' => 'tha', 'THA.LOC104822496' => 'tha', 'Thecc.01G221800' => 'tca', 'Thecc.02G366100' => 'tca', 'Thecc.06G224300' => 'tca', 'Thecc.07G032800' => 'tca', 'Thhalv10003268m.g' => 'esa', 'Thhalv10004894m.g' => 'esa', 'Thhalv10008726m.g' => 'esa', 'Thhalv10021483m.g' => 'esa', 'Thhalv10021737m.g' => 'esa', 'Thhalv10022940m.g' => 'esa', 'TPR.G1149' => 'tpr', 'TPR.G4187' => 'tpr', 'TPR.G4616' => 'tpr', 'TPR.G6415' => 'tpr', 'TPR.G7470' => 'tpr', 'TWI36G0690' => 'twi', 'TWI36G0973' => 'twi', 'TWI38G0001' => 'twi', 'TWI38G0419' => 'twi', 'TWI38G1396' => 'twi', 'TWI63G1587' => 'twi', 'TWI75G1046' => 'twi', 'TWI75G1294' => 'twi', 'unitig_746.g26590' => 'ugi', 'unitig_8.g3533' => 'ugi', 'unitig_899.g15415' => 'ugi', 'vmacro02219' => 'vma', 'vmacro02778' => 'vma', 'vmacro03677' => 'vma', 'vmacro09338' => 'vma', 'vmacro12192' => 'vma', 'vmacro12193' => 'vma', 'vmacro14005' => 'vma', 'VMungo0331G0409' => 'vmu', 'VMungo0540G0149' => 'vmu', 'VMungo0647G1441' => 'vmu', 'VMungo1080G0870' => 'vmu', 'VMungo1127G1526' => 'vmu', 'VMungo1383G0083' => 'vmu', 'VMungo1383G3571' => 'vmu', 'Zm00001eb064470' => 'zma', 'Zm00001eb210810' => 'zma', 'Zm00001eb237890' => 'zma', 'Zm00001eb281490' => 'zma', 'Zm00001eb284960' => 'zma' ) $gf_id = 'HOM05D001148' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001148' ) $data_identifier = 'HOM05D001148' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 5, 'amhyb' => (int) 6, 'aly' => (int) 6, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 4, 'cqu' => (int) 8, 'bca' => (int) 9, 'bol' => (int) 6, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 4, 'car' => (int) 6, 'ccan' => (int) 4, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 6, 'din' => (int) 7, 'dzi' => (int) 9, 'eca' => (int) 5, 'bvu' => (int) 5, 'egr' => (int) 4, 'fan' => (int) 14, 'fve' => (int) 5, 'gma' => (int) 10, 'ghi' => (int) 17, 'gra' => (int) 7, 'vvi' => (int) 5, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 13, 'lonja' => (int) 9, 'lja' => (int) 5, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 9, 'mtr' => (int) 5, 'cme' => (int) 9, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 11, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 5, 'pax' => (int) 6, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 4, 'pso' => (int) 4, 'qlo' => (int) 11, 'rch' => (int) 5, 'rsi' => (int) 8, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 5, 'sas' => (int) 5, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 6, 'tpr' => (int) 5, 'twi' => (int) 8, 'ugi' => (int) 3, 'vma' => (int) 7, 'vmu' => (int) 7, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb284960' $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